rs1407709

Variant names:

• chr1-188093548-T-C
• rs1407709
• ENST00000648838.2:n.455-3591T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648838.2(ENSG00000285894):​n.455-3591T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,090 control chromosomes in the GnomAD database, including 45,608 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.77 (45608 hom., cov: 31)
• Consequence: ENSG00000285894 ENST00000648838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

Genes affected

ENSG00000285894 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285894	ENST00000648838.2	n.455-3591T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116812 AN: 151972 Hom.: 45554 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.773

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.769 AC: 116922 AN: 152090 Hom.: 45608 Cov.: 31 AF XY: 0.774 AC XY: 57557 AN XY: 74344

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.776

Alfa AF: 0.800 Hom.: 23141

Bravo AF: 0.762

Asia WGS AF: 0.827 AC: 2875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1407709; hg19: chr1-188062679;